chrX-18260273-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_006089.3(SCML2):āc.967A>Gā(p.Ile323Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000334 in 1,196,887 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_006089.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCML2 | NM_006089.3 | c.967A>G | p.Ile323Val | missense_variant | 9/15 | ENST00000251900.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCML2 | ENST00000251900.9 | c.967A>G | p.Ile323Val | missense_variant | 9/15 | 1 | NM_006089.3 | P1 | |
SCML2 | ENST00000665583.1 | c.175A>G | p.Ile59Val | missense_variant | 3/8 |
Frequencies
GnomAD3 genomes AF: 0.0000180 AC: 2AN: 111305Hom.: 0 Cov.: 23 AF XY: 0.0000298 AC XY: 1AN XY: 33541
GnomAD3 exomes AF: 0.00000575 AC: 1AN: 173974Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 59312
GnomAD4 exome AF: 0.00000184 AC: 2AN: 1085530Hom.: 0 Cov.: 27 AF XY: 0.00 AC XY: 0AN XY: 352800
GnomAD4 genome AF: 0.0000180 AC: 2AN: 111357Hom.: 0 Cov.: 23 AF XY: 0.0000298 AC XY: 1AN XY: 33603
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at